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Manager–worker-based model for the parallelization of quantum Monte Carlo on heterogeneous and homogeneous networks

Michael T. Feldmann, Julian C. Cummings, David R. Kent, Richard P. Muller, William A. Goddard
2007 Journal of Computational Chemistry  
A manager-worker-based parallelization algorithm for Quantum Monte Carlo (QMC-MW) is presented and compared with the pure iterative parallelization algorithm, which is in common use.  ...  The new manager-worker algorithm performs automatic load balancing, allowing it to perform near the theoretical maximal speed even on heterogeneous parallel computers.  ...  Special thanks go to Shane Canon and Iwona Sakrejda for providing dedicated computer time on PDSF at NERSC.  ... 
doi:10.1002/jcc.20836 pmid:17918283 fatcat:pac32hsy6fb3fnquirh7m7rxli

Bridging the Gap between Deep Learning and Frustrated Quantum Spin System for Extreme-scale Simulations on New Generation of Sunway Supercomputer [article]

Mingfan Li, Junshi Chen, Qian Xiao, Qingcai Jiang, Xuncheng Zhao, Rongfen Lin, Fei Wang, Hong An, Xiao Liang, Lixin He
2022 arXiv   pre-print
The final achievement demonstrates the effectiveness of CNN-based representation of quantum-state and brings the state-of-the-art record up to a brand-new level from both aspects of remarkable accuracy  ...  Here we present a novel convolutional neural network (CNN) for simulating the two-dimensional highly frustrated spin-1/2 J_1-J_2 Heisenberg model, meanwhile the simulation is performed at an extreme scale  ...  ACKNOWLEDGMENTS We sincerely thank the editors and the reviewers for their careful reading and thoughtful comments.  ... 
arXiv:2108.13830v4 fatcat:hsnlbonfezgmlhbkzzvy7oifli

A Review of Parallel Heterogeneous Computing Algorithms in Power Systems

Diego Rodriguez, Diego Gomez, David Alvarez, Sergio Rivera
2021 Algorithms  
The current computing platforms employed for planning, operation, studies, visualization, and the analysis of power systems are reaching their operational limit since the complexity and size of modern  ...  This paper presents a review of Parallel Heterogeneous Computing techniques, how these techniques have been applied in a wide variety of power system applications, how they help reduce the computational  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/a14100275 fatcat:rzl4kn2xl5cb3phhtxwtmc57iu

Parallel stochastic systems biology in the cloud

M. Aldinucci, M. Torquati, C. Spampinato, M. Drocco, C. Misale, C. Calcagno, M. Coppo
2013 Briefings in Bioinformatics  
The stochastic modelling of biological systems, coupled with Monte Carlo simulation of models, is an increasingly popular technique in bioinformatics.  ...  In particular, the Calculus of Wrapped Components (CWC) simulator for systems biology, which is designed according to the FastFlow pattern-based approach, is presented and discussed.  ...  In [34] , for example, a model of the human liver is emulated in a cloud-based system where each liver lobule is represented by Monte Carlo samples.  ... 
doi:10.1093/bib/bbt040 pmid:23780997 fatcat:j4twwscdvbgjfl7ayapqsdzecu

Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond [article]

Anthony Scemama , William Jalby
2012 arXiv   pre-print
This novel scheme is based on the use of the highly localized character of atomic Gaussian basis functions (not the molecular orbitals as usually done), ii.) the possibility of keeping the memory footprint  ...  These strategies have been implemented in the QMC=Chem code developed at Toulouse and illustrated with numerical applications on small peptides of increasing sizes (158, 434, 1056 and 1731 electrons).  ...  The authors would also like to thank Bull, GENCI and CEA for their help in this project.  ... 
arXiv:1209.6630v2 fatcat:ymr5olx27fby5l5wqcfscsd64y

Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond

Anthony Scemama, Michel Caffarel, Emmanuel Oseret, William Jalby
2013 Journal of Computational Chemistry  
This novel scheme is based on the use of the highly localized character of atomic Gaussian basis functions (not the molecular orbitals as usually done), ii.) the possibility of keeping the memory footprint  ...  These strategies have been implemented in the QMC=Chem code developed at Toulouse and illustrated with numerical applications on small peptides of increasing sizes (158, 434, 1056 and 1731 electrons).  ...  The authors would also like to thank Bull, GENCI and CEA for their help in this project.  ... 
doi:10.1002/jcc.23216 pmid:23288704 fatcat:6sugddhrifffvnznskiog2x3ty

Midpoint routing algorithms for Delaunay triangulations

Weisheng Si, Albert Y. Zomaya
2010 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS)  
Parallelization of DQMC Simulation for Strongly Correlated Electron Systems Abstract Determinant Quantum Monte Carlo (DQMC) simulation has been widely used to reveal macroscopic properties of strong  ...  simplifies the programming of accelerator-based heterogeneous parallel systems.  ...  Abstract Line-rate data traffic monitoring in high-speed networks is essential for network management.  ... 
doi:10.1109/ipdps.2010.5470471 dblp:conf/ipps/SiZ10 fatcat:yuchdc4zp5borm5vs7j4rqgmzy

Expanding the boundaries of ligand–target modeling by exascale calculations

Viacheslav Bolnykh, Giulia Rossetti, Ursula Rothlisberger, Paolo Carloni
2021 Wiley Interdisciplinary Reviews. Computational Molecular Science  
computing, molecular dynamics, ligand-target modeling | INTRODUCTION Modeling plays a key role in drug discovery and design. 1,2 Developing a new drug molecule can cost up to $2.6 billion: the use of computational  ...  The focus is on technical aspects which might not be all that familiar to the computational pharmacologist.  ...  ACKNOWLEDGMENTS We gratefully acknowledge the funding by (a) the Deutsche Forschungsgemeinschaft DFG via the Research Unit  ... 
doi:10.1002/wcms.1535 fatcat:wwu4ixhvhngivkz4olvzm3c6r4

Multiscale modelling of nanostructures

Dimitri D Vvedensky
2004 Journal of Physics: Condensed Matter  
The selfassembly of quantum dot ensembles will be used as a case study for the issues that arise and the methods used for all nanostructures.  ...  Recent efforts have focused on combining traditional methodologies-density functional theory, molecular dynamics, Monte Carlo methods and continuum descriptionswithin a unified multiscale framework.  ...  Acknowledgments This review is based on a series of lectures presented at the UCLA Institute of Pure and Applied Mathematics (IPAM) programme on Mathematics in Nanoscale Science and Engineering in September  ... 
doi:10.1088/0953-8984/16/50/r01 fatcat:lvgfwhob2vbu7ppsmwqvxsswjm

A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative

R. Backofen, H.-G. Borrmann, W. Deck, A. Dedner, L. De Raedt, K. Desch, M. Diesmann, M. Geier, A. Greiner, W. R. Hess, J. Honerkamp, St. Jankowski (+13 others)
2006 PIK - Praxis der Informationsverarbeitung und Kommunikation  
The organizational, technical, and financial components of our framework, the Black Forest Grid Initiative (BFG) are described and results of its implementation are presented.  ...  The classical infrastructure of university computer centres results to be unsuited to cope with the new requirements for a multitude of reasons.  ...  Now the dependency of the reflectance on the optical material parameters can be determined by a Monte-Carlo model simulating the light transport in turbid media.  ... 
doi:10.1515/piko.2006.81 fatcat:ntesur7nfndgtlyle4trttv4yi

Computational Approaches in Theranostics: Mining and Predicting Cancer Data

Tânia F. G. G. Cova, Daniel J. Bento, Sandra C. C. Nunes
2019 Pharmaceutics  
This review describes the recent progress in the development of computational models and methods used to facilitate research on the molecular basis of cancer and on the respective diagnosis and optimized  ...  These approaches have provided invaluable insights for improving the experimental design of therapeutic delivery systems and for increasing the translational value of the results obtained from early and  ...  A combined approach based on computational fluid dynamics and fractal analysis and an image-based lung model, for reflecting the presence and progression of bronchial tumor, was used for evaluating the  ... 
doi:10.3390/pharmaceutics11030119 pmid:30871264 pmcid:PMC6471740 fatcat:f3ktwwwcsvgepiopdhifiglebi

Online codesign on reconfigurable platform for parallel computing

Clément Foucher, Fabrice Muller, Alain Giulieri
2013 Microprocessors and microsystems  
We propose a platform supporting this flow and describe its different implementations used to prove the feasibility of our approach.  ...  In this article, we present an approach allowing a hardware/software codesign of applications in which implementation can be chosen at run time depending on available resources.  ...  [20] use the Cray XD1 to identify the possible gain on executing Quantum Monte Carlo application on reconfigurable supercomputers.  ... 
doi:10.1016/j.micpro.2011.12.007 fatcat:bnvnv5dhongzbaxamkl5tjvezm

E-Cam Dissemination Report

Donal Mackernan, Kate Collins
2016 Zenodo  
This deliverable is a report on the dissemination activities of E-CAM during the first year, regarding (a) the generation and updating of a Wiki (or equivalent) describing E-CAM's activities and, (b) E-CAM  ...  The authors used twenty-four peptides per simulation box in replica exchange Monte Carlo and kinetic Monte Carlo pH-dependent simulations; which is, apparently, the first time that such a large scale approach  ...  In 2016 he started his postdoc at CECAM, EPFL in Lausanne on development and testing of wave and trajectory based methods relevant for studying open quantum system as part of the Work Package 3 "Quantum  ... 
doi:10.5281/zenodo.841756 fatcat:vg7c6g6drvefrno3si7nz4f2eq

Machine Learning in High Energy Physics Community White Paper [article]

Kim Albertsson, Piero Altoe, Dustin Anderson, John Anderson, Michael Andrews, Juan Pedro Araque Espinosa, Adam Aurisano, Laurent Basara, Adrian Bevan, Wahid Bhimji, Daniele Bonacorsi, Bjorn Burkle (+102 others)
2019 arXiv   pre-print
and identify the resource needs for their implementation.  ...  The main objective of the document is to connect and motivate these areas of research and development with the physics drivers of the High-Luminosity Large Hadron Collider and future neutrino experiments  ...  accuracy between Monte Carlo and DNN-based calculations should be undertaken.  ... 
arXiv:1807.02876v3 fatcat:k2fjloakhjcd7lg7may5rtm6ya

Secure, Performance-Oriented Data Management for nanoCMOS Electronics

R. O. Sinnott, C. Bayliss, C. Davenhall, B. Harbulot, M. Jones, C. Millar, G. Roy, S. Roy, G. Stewart, J. Watt, A. Asenov
2008 2008 IEEE Fourth International Conference on eScience  
, and manage the many hundreds of thousands of files and meta-data associated with these simulations.  ...  This scale means that previous assumptions on the uniformity of transistor devices in electronics circuit and systems design are no longer valid, and the industry as a whole must deal with variability  ...  These might be based upon Drift Diffusion approaches solving Poisson's equation, or based on other approaches such as Monte Carlo based ab initio simulations.  ... 
doi:10.1109/escience.2008.21 dblp:conf/eScience/SinnottBDHJMRRSWA08 fatcat:z7igkbupyjb35hjybsw2bpqowm
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